{"id":"https://openalex.org/W2890336406","doi":"https://doi.org/10.1093/bioinformatics/bty784","title":"The GCTx format and cmap{Py, R, M, J} packages: resources for optimized storage and integrated traversal of annotated dense matrices","display_name":"The GCTx format and cmap{Py, R, M, J} packages: resources for optimized storage and integrated traversal of annotated dense matrices","publication_year":2018,"publication_date":"2018-09-08","ids":{"openalex":"https://openalex.org/W2890336406","doi":"https://doi.org/10.1093/bioinformatics/bty784","mag":"2890336406","pmid":"https://pubmed.ncbi.nlm.nih.gov/30203022"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty784","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty784","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/8/1427/28500766/bty784.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/8/1427/28500766/bty784.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5009677333","display_name":"Oana M. Enache","orcid":"https://orcid.org/0000-0002-9541-0058"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"funder","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Oana M Enache","raw_affiliation_strings":["The Broad Institute, Cambridge, MA, USA"],"affiliations":[{"raw_affiliation_string":"The Broad Institute, Cambridge, MA, USA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078970169","display_name":"David L. Lahr","orcid":"https://orcid.org/0000-0001-6283-0286"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"funder","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David L Lahr","raw_affiliation_strings":["The Broad Institute, Cambridge, MA, USA"],"affiliations":[{"raw_affiliation_string":"The Broad Institute, Cambridge, MA, USA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5119011497","display_name":"Ted Natoli","orcid":null},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"funder","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ted E Natoli","raw_affiliation_strings":["The Broad Institute, Cambridge, MA, USA"],"affiliations":[{"raw_affiliation_string":"The Broad Institute, Cambridge, MA, USA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039667883","display_name":"Lev Litichevskiy","orcid":"https://orcid.org/0000-0002-0510-4509"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"funder","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lev Litichevskiy","raw_affiliation_strings":["The Broad Institute, Cambridge, MA, USA"],"affiliations":[{"raw_affiliation_string":"The Broad Institute, Cambridge, MA, USA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037862554","display_name":"David Wadden","orcid":null},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David Wadden","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063882098","display_name":"Corey Flynn","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Corey Flynn","raw_affiliation_strings":["MediaSilo, Boston, MA, USA"],"affiliations":[{"raw_affiliation_string":"MediaSilo, Boston, MA, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017181752","display_name":"Joshua Gould","orcid":"https://orcid.org/0000-0001-9581-5461"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"funder","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joshua Gould","raw_affiliation_strings":["The Broad Institute, Cambridge, MA, USA"],"affiliations":[{"raw_affiliation_string":"The Broad Institute, Cambridge, MA, USA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012209649","display_name":"Jacob K. Asiedu","orcid":null},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"funder","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jacob K Asiedu","raw_affiliation_strings":["The Broad Institute, Cambridge, MA, USA"],"affiliations":[{"raw_affiliation_string":"The Broad Institute, Cambridge, MA, USA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000381800","display_name":"Rajiv Narayan","orcid":null},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"funder","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rajiv Narayan","raw_affiliation_strings":["The Broad Institute, Cambridge, MA, USA"],"affiliations":[{"raw_affiliation_string":"The Broad Institute, Cambridge, MA, USA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5109532899","display_name":"Aravind Subramanian","orcid":null},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"funder","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Aravind Subramanian","raw_affiliation_strings":["The Broad Institute, Cambridge, MA, USA"],"affiliations":[{"raw_affiliation_string":"The Broad Institute, Cambridge, MA, USA","institution_ids":["https://openalex.org/I107606265"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5109532899"],"corresponding_institution_ids":["https://openalex.org/I107606265"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.6908,"has_fulltext":true,"cited_by_count":58,"citation_normalized_percentile":{"value":0.91175394,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"35","issue":"8","first_page":"1427","last_page":"1429"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.998199999332428,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9973000288009644,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8327760696411133},{"id":"https://openalex.org/keywords/serialization","display_name":"Serialization","score":0.7818935513496399},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.7331271171569824},{"id":"https://openalex.org/keywords/suite","display_name":"Suite","score":0.5840395092964172},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.5552409291267395},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.5304763913154602},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5136803984642029},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.49405911564826965},{"id":"https://openalex.org/keywords/software-suite","display_name":"Software suite","score":0.46324387192726135},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.44621849060058594},{"id":"https://openalex.org/keywords/file-format","display_name":"File format","score":0.44502636790275574},{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.44378215074539185},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.39152634143829346},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.3744738698005676},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3710213303565979},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.17032691836357117}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8327760696411133},{"id":"https://openalex.org/C52723943","wikidata":"https://www.wikidata.org/wiki/Q1127410","display_name":"Serialization","level":2,"score":0.7818935513496399},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.7331271171569824},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.5840395092964172},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.5552409291267395},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.5304763913154602},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5136803984642029},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.49405911564826965},{"id":"https://openalex.org/C2778736646","wikidata":"https://www.wikidata.org/wiki/Q1143070","display_name":"Software suite","level":3,"score":0.46324387192726135},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.44621849060058594},{"id":"https://openalex.org/C97250363","wikidata":"https://www.wikidata.org/wiki/Q235557","display_name":"File format","level":2,"score":0.44502636790275574},{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.44378215074539185},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.39152634143829346},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.3744738698005676},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3710213303565979},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.17032691836357117},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty784","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty784","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/8/1427/28500766/bty784.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30203022","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30203022","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:5463826","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6477971","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty784","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty784","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/8/1427/28500766/bty784.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.5600000023841858,"display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G7693037837","display_name":null,"funder_award_id":"U54HL127366","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7766023480","display_name":null,"funder_award_id":"U01HG008699","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320338403","display_name":"Common Fund","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2890336406.pdf","grobid_xml":"https://content.openalex.org/works/W2890336406.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W2001811698","https://openalex.org/W2010457001","https://openalex.org/W2100619498","https://openalex.org/W2119676748","https://openalex.org/W2121604817","https://openalex.org/W2146264532","https://openalex.org/W2150926065","https://openalex.org/W2167395325","https://openalex.org/W2285216336","https://openalex.org/W2509141893","https://openalex.org/W2604527271","https://openalex.org/W2612467560","https://openalex.org/W2768977980"],"related_works":["https://openalex.org/W2150599425","https://openalex.org/W2902536138","https://openalex.org/W2324218546","https://openalex.org/W3012289554","https://openalex.org/W2584052712","https://openalex.org/W2159912353","https://openalex.org/W2308359027","https://openalex.org/W2461542739","https://openalex.org/W2604944932","https://openalex.org/W3209257682"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":11},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}